Unknown is what type of contract you have with the builder, all states vary and only giving you thoughts.
If I understand correctly, you are in contract and these features are part of the house, final inspection has turned up issues that was supposed to come with the house.
If so, no problem. Builder will have to do your granite and A/C unit, it really should not even be a concern from ANY reputable builder.
You state you rather not have those features and will accept $5000. instead, the dollar amount sounds reasonable to most people but very well maybe on the high side.
Here is why the builder may OR may not take your offer.
1. Its possible those features A/C and granite were completely the fault/error of the company involved installing them (supplier/subcontractor). The builder can call them and say, hey you made a mistake, go fix it, in that case it cost the builder nothing but a phone call.
2. It is possible someone in the builders office made the mistake, then, it would fall on the builder.
3. It could be a combination of the above or some degree of it. So hard to put a price tag right now on an unknown.
Depending on the size of the home, it doesnt cost half as much for those features as most people think. But, the builder may concede the 5k to get something closed quickly whether or not his fault and also penalize the sub contractor.
If I was in your shoes and really didnt want the granite and AC unit 5k would be a starting point but dont be disappointed if its turned down and be thrilled if it is accepted.
Personally, thinking of resale, I rather have the granite and AC.